NHS England Data Science PhD Internships

Towards a Documentation Standard and Metadata API for Agent Based Models in Healthcare

Keywords: Simulation, AgentBasedModelling, MultiModalData

Need: In general, ABMs have a solid methodological foundation. However, the implementation and subsequent documentation is inconsistent. For researchers, documenting the degrees of freedom in ABMs is not a primary focus. As such, bespoke models do not explain or share how:

Pertinent information can be captured by a polyglot library that provides metadata about an ABM at runtime and on completion. The ability to describe, annotate and introspect ABM models at runtime, via an opinionated framework, would go a long way in providing standard outputs to validate research and determine the veracity of the model. As well as, documenting the implementation of a particular ABM.

Current Knowledge/Examples & Possible Techniques/Approaches: Currently, documentation is disseminated through articles, conference proceedings or wikis. The models are shared via GitHub, GitLab and OpenABM/CoMSES. The models are written in many languages. As such, the requisite familiarity with the programming language (or tool e.g. NetLogo) used to implement the model is a significant barrier to entry.

Using standardised description formats such as the ‘Overview, Design concepts and Details’ (ODD) protocol is also promoted in the literature. A possible approach would be to implement a library that can generate metadata (at runtime) and a manifest (after each run) for any model with a framework utilising a standardised description protocol.

See for instance the paper Comprehensive and Comprehensible Data Catalogs

Related Previous Internship Projects: N/A as first iteration of the project

Enables Future Work: We aim to use the output of this research for the ABM engine and SynPathGo.

Outcome/Learning Objectives: A possible outcome of this project is a library framework for documenting and labelling ABMs with information at rest and at runtime to generate metadata and a manifest after running the simulation.

Datasets: The project will require existing simulation models in Python to compare the existing documentation against the metadata output.

Desired skill set: Proficient in:

Familiar with:

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